Characterization of the Bellevalia sarmatica (Georgi) Woronov populations from Volgograd oblast using molecular genetic identification

DNA samples obtained from the populations of the Red Data Book species Bellevalia sarmatica (Georgi) Worovow from Volgograd oblast were examined using RAPD and AFLP analyses. DNA marking revealed considerable differences in the levels of interpopulation and intraspecific polymorphisms the Bellevalia. Furthermore, RAPD analysis, despite of lower levels of interpopulation polymorphism identified, made it possible to obtain clearer data on population subdivision upon statistical treatment of the results. The results of this study can be used in developing conservation strategies for maintenance of the species abundance and genetic diversity, as well as in elaborating the criteria for construction genetic collections.     

Molecular phylogeny of mangroves. VI. Intraspecific genetic variation in mangrove species Excoecaria agallocha L. (Euphorbiaceae).

Genomic DNA from 84 individuals of Excoecaria agallocha from seven mangrove populations were analysed for random amplified polymorphic DNAs (RAPDs) using 16 random 10-mer primers. Polymorphism within populations varied from 20% to 31%. At the interpopulation level, 111/149 (74%) of RAPDs were polymorphic. Restriction fragment length polymorphism (RFLP) analysis of 21 individuals (3 individuals randomly selected from the 7 populations) using 30 probe-enzyme combinations revealed a high level of interpopulation polymorphism (62.2%) indicating interpopulation genetic divergence. The polymorphic RAPDs and RFLPs were pooled, and clustering was carried out based on mean similarity for individual populations. The dendrogram showed groupings of populations from the West and East Coasts of India into separate clusters, at 60% similarity level. Further, RAPD and RFLP analysis of male and female plants showed approximately the same level of variation in both sexes, and no sex-linked markers were found. These results demonstrate that considerable intrapopulation and interpopulation genetic variations exist in E. agallocha, and that lack of genetic variation is not the reason for the morphological uniformity observed across the range of the species.     

Genetic variation of Marchalina hellenica (Hemiptera: Margarodidae) sampled from different hosts and localities in Greece

Random amplified polymorphic DNA (RAPD) analysis was applied to 120 individuals of Marchalina hellenica (Gennadius) representing six populations collected in northern, central and southern mainland Greece. One population was sampled on one species of fir tree and the others on two species of pine trees. Four random decamer primers were used to evaluate genetic variation among the populations examined. The results revealed intra- and interpopulation polymorphism both related to host type and region of origin. Phylogenetic analysis based on genetic distances estimated by the RAPD frequencies revealed an important genetic differentiation in samples collected on fir trees in southern Greece and to a lesser extent in samples from pine trees in central and northern Greece. Furthermore, considerable subdivision and restricted gene flow among the populations examined were observed. The results are discussed in relation to the biology and geographical distribution of M. hellenica in Greece.     

Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species

Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers are being used widely for evaluating genetic relationships of crop germplasm. Differences in the properties of these two markers could result in different estimates of genetic relationships among some accessions. Nuclear RFLP markers detected by genomic DNA and cDNA clones and RAPD markers were compared for evaluating genetic relationships among 18 accessions from six cultivated Brassica species and one accession from Raphanus sativus. Based on comparisons of genetic-similarity matrices and cophenetic values, RAPD markers were very similar to RFLP markers for estimating intraspecific genetic relationships; however, the two marker types gave different results for interspecific genetic relationships. The presence of amplified mitochondrial and chloroplast DNA fragments in the RAPD data set did not appear to account for differences in RAPD- and RFLP-based dendrograms. However, hybridization tests of RAPD fragments with similar molecular weights demonstrated that some fragments, scored as identical, were not homologous. In all these cases, the differences occurred at the interspecific level. Our results suggest that RAPD data may be less reliable than RFLP data when estimating genetic relationships of accessions from more than one species.     

大鼠RAPD标记的观察

采用随机扩增多态ＤＮＡ（ＲＡＰＤ）技术,分析ＳＤ和Ｗｉｓｔａｒ二种大鼠的基因多态性,探讨用ＲＡＰＤ标记鉴别二种大鼠及其血标本实验中的认证,结果表明,二种大鼠表现出了各自不同的多态性ＲＡＰＤ标记,作为大鼠的分子标记,可在基因水平区别二种大鼠,故认为是一种大鼠研究的分子依据。     

Assessment of genetic diversity in 31 species of mangroves and their associates through RAPD and AFLP markers

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to assess the genetic diversity in 31 species of mangroves and mangrove associates. Four AFLP primer combinations resulted in the amplification of 840 bands with an average of 210 bands per primer combination and 11 RAPD primers yielded 319 bands with an average of 29 bands per primer. The percentage of polymorphism detected was too high indicating the high degree of genetic variability in mangrove taxa both at inter- and intra-generic levels. In the dendrogram, species belonging to a particular family/ genus, taxa inhabiting similar habitats or having similar adaptations tended to be together. There were exceptions too; as many unrelated species of mangroves form clusters. The intrafamilial classification and inter-relationships of genera in the family Rhizophoraceae could be confirmed by molecular analysis. Both the markers RAPD and AFLP were found equally informative and useful for a better understanding of the genetic variability and genome relationships among mangroves and their associated species.     

Variability of size-age indices and genetic variability of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> from the Western Coast of Kamchatka: Comparative analysis of methods of differentiation of local populations

Study of variability of size-age indices and polymorphism of 6 microsatellite loci, 5 loci of SNP, and accidentally amplified polymorphic DNA (RAPD) of sockeye salmon Oncorhynchus nerka of three largest populations from the western coast of Kamchatka Peninsula was performed. The efficiency of using different types of markers for the differentiation of populations and determination of the population belonging of sockeye salmon from lake-river systems of western Kamchatka was analyzed. Significant interpopulation differences were revealed from the frequencies of alleles of genetic markers and from a set of biological indices. It was established that genetic markers are characterized by a better differentiating capacity, as compared to biological characteristics. The most satisfactory results during determination of population belonging of sockeye salmon were obtained using an integrated data base of allele frequencies of microsatellite and SNP loci.     

10种冬青属植物遗传多样性RAPD和AFLPs分析

采用RAPD和AFLP技术,对10种冬青属植物基因组进行DNA片段扩增,以研究该属种间遗传多样性.结果表明:在RAPD分析中,通过对100种10个碱基随机引物的筛选,发现11种引物能得到多态性较高扩增产物,11种引物共扩增出301条多态性条带,多态率为98.63%.在AFLP分析中,3对选择性引物组合均扩增出了丰富的多态性片段.利用RAPD和AFLP技术分析,结果按UPGMA类平均法进行聚类,聚类结果显示冬青和代茶冬青,木姜冬青和浙江冬青以及光枝刺缘冬青与毛枝三花冬青之间的亲缘关系最近.     

Genotyping of Ganoderma species by improved random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis

Species of Ganoderma are used in traditional medicines. An improved random amplified polymorphic DNA (RAPD) analysis, where the RAMP time is prolonged, has been used to characterize the genetic variation in some well known species of Ganoderma. The DNA materials were collected from ten Ganoderma strains, amplified with randomly selected 24 RAPD primers and evaluated by agarose gel electrophoresis. A cluster dendrogram was constructed for genetic analysis on the basis of amplification results. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 316 bands were found with 93% polymorphism. There was a significant genetic distance between the different strains of Ganoderma, with an index of similarity coefficient in the range of 0.52–0.74. The inter-simple sequence repeat (ISSR) analysis of the Ganoderma DNA samples showed similar trend results to the RAPD analysis with 0.49–0.81 similarity coefficients. This study reports the high level of genetic differences between different species or strains of a single species of Ganoderma and confirms the significance of the improved RAPD method in genetic characterization of organisms. Therefore, the improved RAPD combined with ISSR techniques might be used for the genetic characterization of organisms.     

Genomic relations among two non-mangrove and nine mangrove species of Indian Rhizophoraceae

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to study the genomic relationship among 11 members of Indian Rhizophoraceae represented by nine true mangroves and two non-mangrove species. The AFLP and RAPD bands were scored and analyzed for genetic similarities and cluster analysis was done which separated the 11 species studied into two main groups, the true mangroves and the non-mangroves. The polymorphism observed for these markers showed a high degree of genetic diversity among the constituent taxa of the family. The phylogenetic relationship inferred from molecular marker systems supported the traditional taxonomic classification of the family Rhizophoraceae based on morphological characters at the levels of tribe, phylogeny and delimitation of genera and species, except the intra-generic classification of the genus Bruguiera and the placement of Rhizophora in the family Rhizophoraceae.     

Assessment of genetic polymorphism in Colorado potato beetle Leptinotarsa decemlineata 8Say) by RAPD markers

Four decanucleotide primers were chosen to detect polymorphism for randomly amplified polymorphic DNA (RAPD) in the populations of Colorado potato beetle. The variability of RAPD patterns was studied in three oblasts (Kiev, Moscow and Kurgan) that are geographically distant and considerably differ in ecological and climatic conditions affecting the development of this beetle: Kiev, Moscow, and Kurgan oblasts. A high level of intrapopulation polymorphism exceeding interpopulation differences was revealed. RAPD-marker subsets differing in the frequency and distribution throughout the studied populations were revealed.     

用RAPD和AFLP的方法对中国卤虫(Artemia)种及亲缘关系的研究

利用ＲＡＰＤ（随机扩增多态ＤＮＡ）和ＡＦＬＰ（扩增片段长度多态性）技术对不同种及种群卤虫的关系进行分析。 １０１个随机引物对４种卤虫Ａｆｒａｎｃｉｓｃａｎａ、Ａ ｕｒｍｉａｎａ、Ａ ｓｉｎｉｃａ和Ａ．ｐａｒｔｈｅｎｏｇｅｎｅｌｉｃａ基因组ＤＮＡ进行扩增,平均每个种获得７５１条带,其中４５８条带为多态性标记,每个引物提供平均７４个标记信息,聚类结果表明Ａ．ｓｉｎｉｃａ是不同于其他旧大陆两性生殖卤虫的一个独立的种。对来自 １５个种及品系的卤虫的 ＡＦＬＰ分析显示了非常好的遗传多态性,采用 １２对引物检测到 ５９４条带,其中 ４８０个为多态性标记。聚类结果表明来自西藏的两性生殖卤虫为不同于中国内陆两性生殖卤虫的新种。而孤雌生殖卤虫在进化过程中可能是多源的,中国内陆和沿海的孤雌生殖卤虫是沿着不同的途径进化的,内陆和沿海的孤雌生殖卤虫可能为不同的种。     

RAPD markers for constructing intraspecific tomato genetic maps

The existing molecular genetic maps of the tomato, Lycopersicon spp, are constructed based on isozyme and RFLP polymorphisms between tomato species. These maps are useful for certain applications but have few markers that exhibit sufficient polymorphisms for intraspecific analysis and manipulations within the cultivated tomato. The purpose of this study was to investigate the relative potential of RAPD technology, as compared to isozymes and RFLPs, to generate polymorphic DNA markers within cultivated tomatoes. Sixteen isozymes and 25 RFLP clones that were known to detect polymorphism between L. esculentum and L. pennellii, and 313 random oligonucleotide primers were examined. None of the isozymes and only four of the RFLP clones (i.e., 16%) revealed polymorphism between the cultivated varieties whereas up to 63% of the RAPD primers detected one or more polymorphic DNA fragments between these varieties. All RAPD primers detected polymorphism between L. esculentum and L. pennellii genotypes. These results clearly indicate that RAPD technology can generate sufficient genetic markers exploiting sequence differences within cultivated tomatoes to facilitate construction of intraspecific genetic maps.Abbreviations RFLP restriction fragments length polymorphism - RAPD random amplified polymorphic DNA - PCR polymerase chain reaction - QTLs quantitative trait loci     

Intraspecific genetic polymorphism of Russian sturgeon <Emphasis Type="Italic">Acipenser gueldenstaedtii</Emphasis>

Three populations (Azov, Caspian, and Black Sea) of Russian sturgeon Acipenser queldenstaedtii were tested for polymorphism at nuclear (RAPD and microsatellites) and mitochondrial (PCR identification of two mitotypes) markers. In addition, morphometric analysis of he representatives of Azov population was carried out. According to the morphological characters, the Black Sea population occupied an intermediate position between the Caspian and Azov populations, reflecting the phylogeography of this species. In agreement with the morphometric data, genetic distances (the data of STR analysis) also placed the Black Sea population between the Caspian and Azov populations (F _ST = 0.058 and 0.043). The genetic distance between the Azov and Caspian population was somewhat higher (F _ST = 0.070). The highest allelic polymorphism at four microsatellite loci was found observed in Caspian population, while the lowest polymorphism was in the Sea of Azov. RAPD analysis distinguished high polymorphism within the populations, although it was not feasible for interpopulation analysis. Using the method differentiating the “baerii-like” and typical “gueldenstaedtii” mitotypes, the absence of the “baerii-like” marker in the Black Sea population was demonstrated. The frequency of this marker in Caspian and Azov populations constituted 31.1 and 1.8%, respectively. Possible evolutionary reasons for the interpopulation differences observed are discussed.     

Analysis of tetraploid Elymus species using wheat microsatellite markers and RAPD markers.

An analysis of Amplification fragment polymorphism of DNA from 27 accessions of 19 tetraploid Elymus species was carried out using 18 wheat microsatellite (WMS) primer pairs and 10 decamer primers. Ten WMS primer pairs produced multiple polymorphism on all accessions tested. Two independent phenograms, one based on WMS-PCR and one on RAPDs, separated the 19 tetraploid species into two main groups, viz., the SH genome species group and the SY genome species group. The results coincide with the genomic classification of these species and hence support previous studies showing that Elymus is not a monophyletic genus. The assays indicated that accessions within a species cluster together, which concurs with the morphological classification. Interspecific and intraspecific polymorphisms were detected by the WMS-PCR and RAPD analyses. Variation was observed among accessions of Elymus caninus. The WMS-PCR detected a much higher level of polymorphism than the RAPD analysis. WMSs seem to be more efficient markers than RAPD markers for studying the population diversity of Elymus species. The potential of cross-species amplification of microsatellite markers as an additional source for genetic analysis and applications in Elymus is discussed in the context of these results.     

Genetic and geographic polymorphism of cultivated tobaccos (Nicotiana tabacum) in Turkey

Nicotiana tabacum (2n = 48) is a natural amphidiploid and shows a distribution over a geographical area in eastern anatolia. Random amplified polymorphic DNA (RAPD) technique was used to evaluate both genetic diversity among 21 primitive tobacco accessions comparing flue cure virginia genotype (FCV) and their geographical polymorphism as a source of genetic variations for breeding programs. Only 13 of all the 60 random primers used in RAPD showed polymorphism acceptable for characterization of these accessions. Totally 118 RAPD fragments were generated from thirteen decamer primer and sixtyfour of them were found polymorphic (54.2%). Mus and FCV showed the smallest genetic distance among accessions cultivated in the eastern anatolia. These results shows that the RAPD assay is a powerful approach for identifying genetic and geographic polymorphism.     

RAPD technique is a useful tool to distinguish Penicillium species.

Random amplified polymorphic DNA (RAPD) analysis was used to evaluate genetic diversity among 13 soil Penicillium strains originating from widely dispersed areas. Twenty one of the 34 synthetic random primers were found to identify polymorphism in amplification products. The results show a high level of diversity of RAPD markers among the strains. All the strains could be identified by their characteristic amplification profile, using selected random primers. This suggests that RAPD analysis is a useful and reliable assay for characterizing the species of Penicillium genus.     

Biochemical and Molecular Characterization of Some Centaurea Species Growing in the Eastern Anatolia Region of Turkey

Random amplified polymorphic DNA (RAPD) and fatty acid (FAME) profiles were used to examine phenotypic and genetic relationships among 16 Centaurea species growing wild in the eastern Anatolia region of Turkey. Thirteen decamer primers were used to examine polymorphism. According to the RAPD results, 99 amplicons in the size range of 50–1000 bp were produced from 13 primers in 16 Centaurea species. Genetically four distinct groups were determined among the species of Centaurea, which represents high genetic variation. In the 16 species, 14 fatty acids were determined according to FAME results. Both FAME and RAPD results showed that C. virgata is genetically different from other species. The differences in the composition of fatty acids among Centaurea species suggest that fatty acid profiles could be used to differentiate among some of these species. Results of this study show that RAPD and FAME analyses are consistent.     

GENETIC DIVERSITY OF FIVE FRESHWATER MUSSELS IN GENUS ANODONTA (MOLLUSCA: BIVALVIA) REVEALED BY RAPD ANALYSIS

Unionidae(Bivalvia)are distributed infreshwaters,and represent a significanttaxonof benthic community[1].In China,freshwater mussels are abundant resources[2].Since1949,substantial investigations onthe unionidfau-na had been undertakenin China[3—8].Withreference tooverseas research[9,10],a preliminary reorganization onthe Unionidae was performed accordingtosome classifica-tion characteristics such as shell shape,larvae character-istics,and breeding habit[11].Due tothe serious conver-gence of freshwater muss...     

通过RAPD分析揭示五种淡水无齿蚌（软体动物门：双壳类）的遗传多样性

Unionidae(Bivalvia)are distributed infreshwaters,and represent a significanttaxonof benthic community[1].In China,freshwater mussels are abundant resources[2].Since1949,substantial investigations onthe unionidfau-na had been undertakenin China[3—8].Withreference tooverseas research[9,10],a preliminary reorganization onthe Unionidae was performed accordingtosome classifica-tion characteristics such as shell shape,larvae character-istics,and breeding habit[11].Due tothe serious conver-gence o…